My DD was also diagnosed with a Milk Protein allergy. I have read that it takes 2 weeks to get out of my system and then another 2 weeks to get out of her system. We are on week 3. Poops are still super runny or mucussy (sp). We are using Similac Alimentum on the nights my milk can't keep up with her hunger. Be careful using soy. If their systems can't digest milk protein then soy protein can also be a problem. Rice Milk and rice cheese is a safer bet. I have been getting faux dairy cheese, milk and icecream at my local health food store.